Enabling Horizon Workspace manageability should not change the package's behavior. Therefore I would recommend to run tests without enabling Horizon Workspace manageability. There is no way executing a ThinApp package with Horizon Workspace manageability activated without having Horizon Agent locally installed and being entitled.
Once the tests have been conducted you can activate Horizon Workspace manageability by modifying the package.ini or running relink.exe -h.
Same thing regarding testing update packages. Verify the functionality without Horizon Workspace manageability active and then turn Horizon Workspace manageability on.